ROI Properties and Settings

List of ROIs

All regions of interest that are available are listed in the top section of the Data Properties and Settings panel.

Click the Regions of Interest icon at the top of the Data Properties and Settings panel to see the available ROIs (see Filters for information about filtering the listed items).
Click the Eye icon on the left side of a listed item to show or hide the region of interest in the 2D view of the current scene.
Click the 3D icon to show or hide the ROI in the 3D view of the current scene.
Click the Color box to change the highlight color applied to the region of interest. You should note that the color box indicates the currently selected color, as well as the color with the selected opacity applied.
Select a region of interest to view basic information about the ROI and its statistical properties (see Basic Properties and Statistical Properties) and access settings to modify its appearance in views (see 2D Settings, Opacity and Color, and Clip). Right-click a region of interest to access analysis and other functions (see ROI Pop-Up Menu).

See Visibility and Color/LUT Controls for information about renaming and copying ROIs.

You can toggle the visibility and opacity of selected objects in 2D views with the available keyboard shortcuts (see Visibility and Opacity Toggles).

Basic Properties

The information available for a selected region of interest in Basic properties includes its geometry, voxel count, and volume.

Basic properties
	Description
Width	Is the total number of pixels along the X-axis and its physical dimension*.
Height	Is the total number of pixels along the Y-axis and its physical dimension*.
Depth	Indicates the total number of pixels along the Z-axis and its physical dimension*.
Time steps	Indicates the size of the time (T) dimension.
Total voxels	Indicates the total number of voxels in the region of interest. Calculated as widthheightdepth*(time steps).
Volume	Indicates the total volume occupied by the region of interest. Calculated as voxels*(pixel size cubed).

* Calculated as pixels ´ spacing.

Statistical Properties

The information available for a selected region of interest in Statistical properties includes the surface of all labeled voxels within the ROI, as well as the percentage of that surface within the shape that defines the geometry of the ROI. Other statistics include the minimum, maximum, and mean values of the labeled voxels that correspond to a selected dataset. You can also compare the surface of a selected region of interest with another ROI.

Statistical properties

ROI statistical properties
	Description
Labeled voxels	Indicates the total number of voxels that are labeled within the ROI.
Volume (labeled voxels)	Is the volume of all labeled voxels in the selected region of interest. Percentage volume… Is the comparative percentage of the volume of labeled voxels (all values that fall within the histogram) and the total number of voxels within the selected region of interest. The total number of voxels is calculated from the shape of the region of interest, and includes both labeled and unlabeled voxels.
Auto refresh	If selected, the number of labeled voxels and the volume of labeled voxels will be updated automatically whenever changes are made to the ROI. Refresh… Lets you manually update the number of labeled voxels and the volume of labeled voxels.
Surface	Is the surface area of the labeled voxels in the selected region of interest, calculated with two methods. Surface (Lindblad 2005)… In this case, measurements of surface area are computed using the Lindblad surface area estimator, as described in Joakim Lindblad, Surface area estimation of digitized 3D objects using weighted local configurations. Image and Vision Computing, 23, 2005, pp 111-122 (DOI:10.1016/j.imavis.2004.06.012). Surface (Lorenson 1987)… In this case, measurements of surface area are computed using the marching cubes algorithm, as described in William E. Lorensen, Harvey E. Cline, Marching Cubes: A High Resolution 3D Surface Construction Algorithm. ACM SIGGRAPH Computer Graphics, 21(4), July 1987, pp 163-169 (DOI:https://doi.org/10.1145/37402.37422). Click the Compute Surface button to compute the surface of the ROI.
Feret diameters*	Provides measurements of the size of the selected region of interest in an arbitrary direction. Min Feret diameter… Indicates the shortest distance between any two points along the boundary of the labeled voxels at an arbitrary angle. Max Feret diameter… Indicates the longest distance between any two points along the boundary of the labeled voxels at an arbitrary angle. Click the Compute Feret Diameter button to compute the Feret diameters of the selected region of interest.
Dataset	Allows you to extract statistics for the selected dataset. The dataset must have the same shape as the selected ROI and values are calculated for the labeled voxels that intersect with the image data. Min…The minimum intensity value, expressed in the native units of the dataset. Max… The maximum intensity value, expressed in the native units of the dataset. Mean… The mean value, expressed in the native units of the dataset. Click the Refresh button to compute or update the dataset statistics. If Auto refresh is checked, information will be updated automatically whenever the selected region of interest is altered.
Comparative volume	Allows you to compare the volume of a selected ROI with the current region of interest. Click the Refresh button to compute or update the volume statistics. If Auto refresh is selected, information will be updated automatically whenever the selected region of interest is altered.
	Click the Copy to Clipboard button to copy the ROI statistical properties to your clipboard, which can then be pasted into another application.

* The Feret diameter, or Feret's diameter, is a measure of an object’s size in an arbitrary direction. This measurement, which can be defined as the distance between the two parallel planes restricting the object perpendicular to that direction, is also sometimes called the caliper diameter as it can refer to the measurement of object size with a caliper. This measure is often used in the analysis of particle sizes in microscopy.

Tools

You can use the Histogram tool that is available in the Tools box to visualize and analyze the distribution of intensity values of image data that corresponds to the labeled voxels of a region of interest (see Analyzing Histograms Extracted From ROIs).

2D Settings

The options in the 2D settings box, shown below, let you change the appearance of ROIs in the 2D view of the current scene.

2D settings

Show only contour… If checked, the highlight applied to the selected ROI will only appear as a contour. You can adjust the thickness of the contour with the Contour thickness slider.

Opacity and Color

The Opacity and color settings let you adjust the appearance of regions of interest in 2D and 3D views.

Settings for 3D Views

In 3D views, you can control how regions of interest appear with the Diffuse, Specular, Highlight, and Labeled data sliders, as well as by applying additional settings, as described below.

Opacity and color settings for 3D views

Opacity and color box

You must make sure that the selected region of interest is visible in both the scene (Eye icon) and in the 3D view (3D icon) to control its appearance. The appearance of a region of interest, or multiple ROIs, can also be adjusted in the Opacity Settings dialog (see Opacity Console).

Opacity and color settings for 3D views
	Description
Use LUT	If checked, the colors of the selected LUT will be mapped to the underlying dataset values. ROI with solid color highlight (left) and with LUT applied (right) Note You can select the required LUT by clicking the region of interest's color box in the Data Properties and Settings object list. LUTs will then be available in the LUT dialog.
Use material	Lets you assign a material preset, such as aluminum, bronze, cobalt, copper, concrete, and gold, to a region of interest. When applied, the selected material preset will override the currently selected color or LUT. Material presets applied to a series of ROIs
Smoothed (global)	This global setting uses reflected light and a kernel for applying smoothing to all regions of interest visible in the selected 3D view. Original ROI (left) and smoothed ROI (right)
Edge contrast (global)	This global setting produces an image in which the edges of regions of interest are emphasized and other features are rendered semi-transparent. Original ROIs (left) and with edge contrast applied (right)
Diffuse	Lets you vary the strength of diffuse light reflected from the surfaces of the region of interest and is a characteristic of light absorbed by surfaces. Increasing this property with the Diffuse slider will result in surfaces being more defined.
Specular	Lets you vary the strength of specular reflections originating from the surfaces of the region of interest and is a characteristic of light reflected from shiny surfaces. Increasing this property with the Specular slider will result in increased reflections.
Highlight	Lets you adjust the opacity of the colored highlight applied to the selected region of interest. At a value of 100%, the highlight will be fully opaque. At a value of 0%, the highlight will be transparent. Original ROI with blue highlight (left) and will no highlight (right)
Labeled data	Lets you adjust the opacity of all image data that is visible in the view and that corresponds to the labeled voxels in the region of interest. At a value of 100%, image data that corresponds to the labeled voxels in the region of interest will be fully opaque. At a value of 0%, it will be transparent. Note You can extract regions of interest so that only the ROIs are visible by reducing the global volume opacity and increasing the labeled data opacity, as shown below. Original ROI with blue highlight (left) and ROI extracted from the image data Controls for adjusting the opacity of image data (Global volume opacity) is available on the Scene's Views Properties panel, as shown below. Additional opacity settings are available in the Opacity Settings dialog (see Opacity Console).

Clip

The tools in the Clip box, shown below, let you clip interactively along orthogonal planes of the selected region of interest in 3D views (see Clip Tool). You can also add and remove clipped regions from regions of interest (see Adding and Removing Clipped Regions), as well as use the Clip tool to crop a region of interest (see Cropping Datasets).

Clip panel

The options in the 3D effects box let you apply a selected visual effect, or a combination of visual effects, to a clipped region of interest in a 3D view. The properties of the visual effects that can be applied to a region of interest are described below.

3D Effects for Regions of Interest

3D effects for regions of interest
	Example	Description
Reference		Clip box and region of interest without any 3D effect applied.
Clip ROI		If selected, all data that corresponds to the region of interest will be clipped. Clipping can be applied inside or outside of the clip box.
Opacity		If selected, the opacity of the data of that corresponds to the region of interest can be modified with the Opacity slider as shown below.
Window Leveling		If selected, new window level values can be applied to map color ramps (LUTs) to physical values (intensity) so the color map is physically representative of the image data. In this case, the highlight applied to the ROI will be removed automatically. The width of the window and its center value can be modified with the sliders, as shown below.